SUMMARY

One of the gff2ps program strenghts is comparing results from different sources, so it is easy to see differences among a genomic sequence annotation and one or more gene prediction programs, including results from other programs such blast (always processing those results and converting to a GFF compliant file suitable for gff2ps of course). Here we are illustrating how we generated the PostScript plots you can find in the Human/Mouse Gene Prediction page. If you have problems when visualizing the PostScript files take a look on the section about using ghostview.

CONTENTS

As example we are using Hsap_BTK files. To avoid that both sgp predictions (for Full Ortologous -FO- and WGS sequences -3X-) collapse on the same track of geneid ones, we replaced 'geneid_v1.0' from source field by 'SGP.3X' and 'SGP.homol' (in 'Hsap_BTK_sgp3X' and 'Hsap_BTK_sgpFO' respectively). Click on the filenames to see their contents.

Customization files and available variables are explained in chapter four of the User's Manual (available from gff2ps home page).

Running gff2ps

There are two basic ways to work on GFF records with gff2ps: you can merge all the GFF records from different sources into a single GFF file or you can split GFF records from different sources into different files. The second approach provides to you the advantage of easily ordering sources in your plots by ordering the different GFF source files in the command-line. You must keep in mind that sources appear on the PostScript figure in the same order as they are given from input (so that we prefer to work with separate files for each source).
If you manage to have a fixed set of sequence, source and feature names, you can define a fixed set of customization variables (as we did in the previous section), and reuse the custom files for all the plots having the same layout but different datasets (and it is easy to automate the process at the command-line/scripts level too).

The following two commands are using the same customization file on different files (for sgp and tblastx sources):

Note that we preserved the sources ordering (annotation, sgp, geneid, genscan, tblastx and repeatmasker). Backslashes ('\') mean, in bash shell, that the command and its parameters are passed in more than one line, so next line is appended to the previous command-line.

The following two commands are using different customization files on the same files:

You can see here how easy is to merge new sources to the final plots and how easy is to change the plot layout when using different customization files. Next table summarizes outputs from each custom file and input dataset: